16-56951227-A-G

Variant names:

• chr16-56951227-A-G
• rs9989419

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.56 in 151,990 control chromosomes in the GnomAD database, including 24,656 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 109 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85044 AN: 151872 Hom.: 24637 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.578

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.560 AC: 85096 AN: 151990 Hom.: 24656 Cov.: 31 AF XY: 0.564 AC XY: 41866 AN XY: 74282

African (AFR) AF: 0.403 AC: 16711 AN: 41458

American (AMR) AF: 0.623 AC: 9510 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.761 AC: 3929 AN: 5166

South Asian (SAS) AF: 0.609 AC: 2933 AN: 4820

European-Finnish (FIN) AF: 0.629 AC: 6643 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41253 AN: 67944

Other (OTH) AF: 0.582 AC: 1226 AN: 2106

Alfa AF: 0.598 Hom.: 97253

Bravo AF: 0.553

Asia WGS AF: 0.692 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.83
DANN	Benign	0.57
PhyloP100		-0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9989419; hg19: chr16-56985139;